Missing Links 2
by Regularamanda
Summary: Missing Links in Sam and Jack's relationship, set in Season 2.
1. Good Day After All

**Set after **_**The Serpent's Lair**_

**Good Day After all**

Colonel Jack O'Neill laughed and wrapped his 2IC in a bear hug.

"We did it." She said laughing as she hugged him back.

"Yes we did." He said laughing with her. He pulled back and grinned at her. Somehow they had managed to destroy two Goa'uld mother ships. And the Space Monkey was fine.

'It's a good day.' Jack thought, as he accepted congratulations from the other members of the SGC.

"You did well SG-1." General Hammond said proudly. "Unfortunately I need to see Captain Carter and Colonel O'Neill in my office, right now." General Hammond walked out of the gateroom, along with most of the other SG teams.

'Okay…not such a good day.' He thought as his grin disappeared Yes they had violated orders but he thought that saving the planet would have gotten them a get out of jail free card. Literally. 'I guess saving the world just doesn't mean as much as it used to.' He though dryly.

Daniel turned worried eyes on them. "They can't seriously think about punishing you, after what we just did."

"We don't know." Jack said with a sigh.

"We better..." Sam said pointing at the door that led out of the gate room.

"Yeah."

~*~*~*~

They both walked into the General's office, nervously.

Okay so at the time she hadn't figure that they would come back alive…but now they were back and the planet was saved and Sam was incredibly nervous. 'You knew this would happen' She told herself. General Hammond was well within his rights to reprimand them.

General Hammond sighed and stood up. "Colonel, Captain, what you did grossly violated orders, I should give you both a Court-Martial."

Jack cut in. "With all due respect sir, Captain Carter had nothing to do with this, I ordered her to come, I thought we would need her."

"Sir…" Sam started to say but stopped with the look that Jack sent her. 'Why did he do that?' She wondered.

"But." General Hammond said continuing "After what you and the rest of SG-1 just did, I can't in good conscious, reprimand you for what you just did. You saved countless millions of lives. But next time please follow my orders. You are dismissed."

Sam and Jack both let out sighs of relief.

"Thank you sir." They both said at the same time, and walked out of the office.

"Well that was a close one." Jack said.

"Yes sir….Colonel why did you tell the General that you ordered me?" She asked.

~*~*~*~

Jack stopped walking and turned around to face her. He couldn't tell her the truth…he couldn't tell her that he had done it because he didn't want to see her career destroyed.

"Because Carter, your too brilliant of a scientist to get reprimanded for something like that. If we would have gotten a Court-Martial, it would have been my fault because I should have ordered you to stay in the first place." Jack said honestly.

'Yup just leave out all those parts about how guilt you would feel to see anything like that happen to her.' Jack thought to himself.

He knew she was a competent soldier. But he wanted to protect her, wanted to keep her safe no matter what.

"Sir…I volunteered." Sam told him.

"Hey can't I just save the damsel in distress for once?" He said teasing her.

"This damsel doesn't needed saving." She said teasing him back.

"That's debatable…said damsel also needs food…you, me, blue Jell-O, commissary in ten minutes?" Jack asked.

Sam sent him a full Carter grin, the kind she gave when she was truly happy. "Yes sir."

Jack swallowed at how beautiful she looked. She was beautiful all the time but when she turned that mega watt smile on, it melted a small part of his heart that he had long thought dead. Jack smiled back at her. It was a good day after all.

~*~*~*~

It was indeed a good day after all. The planet was saved and two friends enjoyed each other's company over a snack. Not much was said, but the unspoken attraction was there, an ever present force in both their lives.

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_Author's Note- So if you notice in this episode at the very end when the camera zooms out, Jack hugs Sam, I could have loved to have seen it more clearly! Thanks for reading and if you liked it let me know!_


	2. Left Behind

_Author's Note- Sorry that it took so long for this chapter to come out. I really hope the next one's will be posted quicker. This is Part 1 of 2._

**Set during **_**In the Line of Duty**_

**Left Behind**

Colonel Jack O'Neill needed something, anything, to get his mind off of his 2IC. History was repeating itself it seemed. Major Kawalsky had been taken as a host by a Goa'uld a year ago and it had dealt him a blow to him but now…with Sam…Jack sighed.

No matter how much he might try to convince himself otherwise, she was more then just his 2IC and friend. He hadn't fully realized that till now. When God knew what might happen to her. They didn't have a way to safely remove the symbiote from Sam.

All Jack really knew was that it wasn't going to end well, and his heart would suffer in the process.

'This can not be happening.' Jack groaned to himself. Finally though, he decided he wanted some answers.

~*~*~*~

Sam wasn't in control of herself. This Goa'uld that was inside of her was. She had never felt like this before. She could scream and will herself to talk but the Goa'uld wouldn't let her.

The door suddenly opened and Jack walked in.

Sam's heart pounded when she saw him. He had been here to see her a few hours ago, and she had convinced herself that she wasn't going to see him again. And yet here he was, he had come back. The question was why.

"I want some answers." He said.

"What about?" The Goa'uld said.

"Why did you choose her?" Jack asked.

"She was the only one there at the time."

"You could have went into someone else…me." Jack said.

Sam felt the Goa'uld inside of her hesitate and felt it's shock at his statement.

"You were not there at that moment." The Goa'uld said.

"I know." Jack whispered, some form of emotion written in his words that Sam couldn't identity. "That one that you're in…she's important…if you're really one of the good guys you'll let her go. She's needed to help fight the Goa'uld."

"Let me go through the stargate." It said.

"I only have your word that you'll bring her back. And I'm not going to risk her not coming back." Jack said firmly.

Jack once again turned to go and Sam was desperate now more then ever. She begged the Goa'uld for control and for once the Goa'uld let her. The symbiote had pretended to be her last time Jack had tried to leave…but this time it was her. Sam realized that it was still in shock that Jack would have willing take the symbiote…so that she wouldn't have to.

"Sir…we don't leave our people behind…please…I'm scared. Please don't go." Sam whispered.

Jack turned around and glanced at her. "If it is you Sam, I'm sorry and if it's not…Go to Hell." He said angrily. And with that he walked out.

The Goa'uld retook control and went back down to the bunk. But inside Sam wept. One of the things that she had always admired about the Colonel…he never left anyone behind. Except, right now, he had.

~*~*~*~

For once he had left one of his own team members behind. And though she was unaware of it at that moment, he'd be back. He'd come back for any one of his team…but he'd _always_ come back for her.

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_Author's Note- As always thanks for reading. And if you liked it and feel so inclined leave me a review!_


	3. No Fear

**No Fear**

Jack sat on the infirmary bed watching Sam sleep. It had been a week since that thing had left her, had given it's life for her. And She still wasn't back to herself yet. Post traumatic syndrome Doctor Frasier had called it. And he figured he wouldn't be back to himself either if he was in her shoes.

But he wanted his 2IC back…wanted his friend back. He played with his yo-yo to pass the time but his eyes couldn't help straying to Sam.

He had been so certain that when he found her that she was dead. She was laying there motionless and he had ran to her, repeating her name over and over again, willing her to breathe. His heart had been in his throat and he had felt like someone had punched him in the gut. He had known it was going to turn out bad, that he would experience pain when it was all said and done. And he had, for the shortest of moments there when he had believed she was dead. If he had lost her…No he didn't want to think about that. Not now when she was alright.

And he couldn't think like that, wasn't supposed to think of her as anything more then a friend and 2IC. He wasn't supposed to consider the possibility that if something had happened to her…his world wouldn't be the same.

She had somehow managed to worm her way into his cold heart, the parts that he had never thought would see the light again.

'Go figure you finally let someone in…and then you almost lose them.' He thought to himself.

Jack sighed and shook his head to clear his thought.

~*~*~*~

Sam thrashed around in the bed, in the middle of a nightmare. The Goa'uld was still in her…it hadn't left. And _he_ had left her behind.

A calming hand touched her shoulder and called her name. "Sam…Sam wake up you're okay." The voice said.

The voice had the power to calm her and she realized whose voice it belonged to. Jack O'Neill.

She slowly opened her eyes and all fear left her as she gazed into his eyes. He was here…he had come back for her…and as long as she was with him, she was safe. He'd been here everyday for the past week. He was there went she went to sleep and he was there when she woke up.

'He'd do that for any one of his team.' She reasoned with herself. It didn't mean he cared for her more because he hadn't left her side.

"You okay?" Jack asked concerned.

"Fine sir." She answered.

"Need anything?" Jack whispered softly.

Sam swallowed and wondered if she should tell him the truth.

"I just need someone…here sir." She answered just as softly.

Jack smiled at her and walked across the room and for a moment she was afraid he was leaving. He came back with a chair and sat it next to her bed. He laid his hand next to hers on the bed, not touching but she could feel the warmth of his hand.

"Go back to sleep." He ordered.

"I'm…afraid." She whispered.

"I'm right here if you need anything…now get some shut eye Captain. Before I have to court martial you."

Sam smiled softly at his joke and slowly closed her eyes. He was right there if she needed him. And as long as she knew that he was there…her nightmares would stay away.

'What about when he's not there?' Her heart cried. She pushed the thought aside. Right now he was by her side…and for now that was enough.

~*~*~*~

What she didn't know was that he'd be by her side for as long as she needed him. And what he didn't know was that slowly and softly his feelings for her were starting to change. Starting to change in something that neither of them were prepared for.

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_Author's Note- Thanks for reading and if you liked it let me know!_


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